To Install erase all the things in your current Index.ini of your base .rte and put:

DataModule
	IncludeFile = Base.rte/Materials.ini
	IncludeFile = Base.rte/Sounds.ini
	IncludeFile = Base.rte/Effects.ini
	IncludeFile = Base.rte/Ammo.ini
	IncludeFile = Base.rte/Devices.ini
	IncludeFile = Base.rte/Actors.ini
	IncludeFile = HaloAI.rte/Effects.ini
	IncludeFile = HaloAI.rte/Grunt.ini
	IncludeFile = HaloAI.rte/Actors.ini
//	IncludeFile = HaloAI.rte/Clones.ini
	IncludeFile = HaloAI.rte/Skelereplace.ini
	IncludeFile = Base.rte/Scenes.ini

And re-name your skeleton to Anything you want,
perferebly Skeleton2 so you can find it easier when buying one.

And rename your Green clone to anything you want, but to make it easier
just make it Green Clone2.

This process will be much easier once the mod is finished and completed.